rs12524865

Variant names:

• chr6-133875536-C-A
• rs12524865
• ENST00000607033.5:n.379+13068G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000607033.5(TARID):​n.379+13068G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,974 control chromosomes in the GnomAD database, including 9,189 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.34 (9189 hom., cov: 31)
• Consequence: TARID ENST00000607033.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.257
• Publications: 26 publications found

Genes affected

TARID (HGNC:50506): (TCF21 antisense RNA inducing promoter demethylation)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.475 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607033.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	NR_109982.1		n.403+13068G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TARID	ENST00000607033.5	TSL:1	n.379+13068G>T		intron	N/A
	TARID	ENST00000419627.2	TSL:5	n.447+13068G>T		intron	N/A
	TARID	ENST00000606544.5	TSL:5	n.379+13068G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51313 AN: 151856 Hom.: 9173 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.490

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.355

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.338 AC: 51368 AN: 151974 Hom.: 9189 Cov.: 31 AF XY: 0.341 AC XY: 25332 AN XY: 74292

African (AFR) AF: 0.413 AC: 17103 AN: 41426

American (AMR) AF: 0.421 AC: 6431 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1199 AN: 3468

East Asian (EAS) AF: 0.491 AC: 2529 AN: 5152

South Asian (SAS) AF: 0.408 AC: 1964 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2360 AN: 10558

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18702 AN: 67972

Other (OTH) AF: 0.359 AC: 758 AN: 2112

Alfa AF: 0.304 Hom.: 22531

Bravo AF: 0.359

Asia WGS AF: 0.448 AC: 1555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.40
PhyloP100		0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12524865;

hg19: chr6-134196674;